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Ghebreamlak S, Stoian SA, Lees NS, Cronin B, Smith F, Ross MO, Telser J, Hoffman BM, Duin EC. The Active-Site [4Fe-4S] Cluster in the Isoprenoid Biosynthesis Enzyme IspH Adopts Unexpected Redox States during Ligand Binding and Catalysis. J Am Chem Soc 2024; 146:3926-3942. [PMID: 38291562 DOI: 10.1021/jacs.3c11674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate reductase, or IspH (formerly known as LytB), catalyzes the terminal step of the bacterial methylerythritol phosphate (MEP) pathway for isoprene synthesis. This step converts (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP) into one of two possible isomeric products, either isopentenyl diphosphate (IPP) or dimethylallyl diphosphate (DMAPP). This reaction involves the removal of the C4 hydroxyl group of HMBPP and addition of two electrons. IspH contains a [4Fe-4S] cluster in its active site, and multiple cluster-based paramagnetic species of uncertain redox and ligation states can be detected after incubation with reductant, addition of a ligand, or during catalysis. To characterize the clusters in these species, 57Fe-labeled samples of IspH were prepared and studied by electron paramagnetic resonance (EPR), 57Fe electron-nuclear double resonance (ENDOR), and Mössbauer spectroscopies. Notably, this ENDOR study provides a rarely reported, complete determination of the 57Fe hyperfine tensors for all four Fe ions in a [4Fe-4S] cluster. The resting state of the enzyme (Ox) has a diamagnetic [4Fe-4S]2+ cluster. Reduction generates [4Fe-4S]+ (Red) with both S = 1/2 and S = 3/2 spin ground states. When the reduced enzyme is incubated with substrate, a transient paramagnetic reaction intermediate is detected (Int) which is thought to contain a cluster-bound substrate-derived species. The EPR properties of Int are indicative of a 3+ iron-sulfur cluster oxidation state, and the Mössbauer spectra presented here confirm this. Incubation of reduced enzyme with the product IPP induced yet another paramagnetic [4Fe-4S]+ species (Red+P) with S = 1/2. However, the g-tensor of this state is commonly associated with a 3+ oxidation state, while Mössbauer parameters show features typical for 2+ clusters. Implications of these complicated results are discussed.
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Affiliation(s)
- Selamawit Ghebreamlak
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Sebastian A Stoian
- Department of Chemistry, University of Idaho, 875 Perimeter Drive, MS 2343 Moscow, Idaho 83844, United States
| | - Nicholas S Lees
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Bryan Cronin
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Forrest Smith
- Department of Drug Discovery & Development, Auburn University, 4306 Walker Building, Auburn, Alabama 36849, United States
| | - Matthew O Ross
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Joshua Telser
- Department of Biological, Chemical and Physical Sciences, Roosevelt University, 430 S. Michigan Avenue, Chicago, Illinois 60605, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
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2
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Brown AC, Suess DLM. Valence Localization in Alkyne and Alkene Adducts of Synthetic [Fe 4S 4] + Clusters. Inorg Chem 2023; 62:1911-1918. [PMID: 35704768 PMCID: PMC9751231 DOI: 10.1021/acs.inorgchem.2c01353] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Reported herein are alkyne and alkene adducts of synthetic [Fe4S4]+ clusters that model intermediates and inhibitor-bound states in enzymes involved in isoprenoid biosynthesis. Treatment of the N-heterocyclic carbene-ligated cluster [(IMes)3Fe4S4(OEt2)][BArF4] (IMes = 1,3-dimesitylimidazol-2-ylidene; [BArF4]- = tetrakis(3,5-bis(trifluoromethyl)phenyl)borate) with phenylacetylene (PhCCH) or cis-cyclooctene (COE) results in displacement of the Et2O ligand to yield the corresponding π complexes, [(IMes)3Fe4S4(PhCCH)][BArF4] and [(IMes)3Fe4S4(COE)][BArF4]. EPR spectroscopic analysis demonstrates that both clusters are doublets with giso > 2 and thus are spectroscopically faithful models of the analogous species characterized in the isoprenoid biosynthetic enzymes IspG and IspH. Structural and Mössbauer spectroscopic analysis reveals that both complexes are best described as [Fe4S4]+ clusters in which the unique Fe site engages in modest back-bonding to the π-acidic ligand. Paramagnetic NMR studies show that, even at room temperature, the alkyne/alkene-bound Fe centers harbor minority spin and therefore adopt an Fe2+ valence. We propose that such valence localization could likewise occur in Fe-S enzymes that interact with π-acidic molecules.
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3
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The Multifaceted MEP Pathway: Towards New Therapeutic Perspectives. Molecules 2023; 28:molecules28031403. [PMID: 36771066 PMCID: PMC9919496 DOI: 10.3390/molecules28031403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Isoprenoids, a diverse class of natural products, are present in all living organisms. Their two universal building blocks are synthesized via two independent pathways: the mevalonate pathway and the 2-C-methyl-ᴅ-erythritol 4-phosphate (MEP) pathway. The presence of the latter in pathogenic bacteria and its absence in humans make all its enzymes suitable targets for the development of novel antibacterial drugs. (E)-4-Hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP), the last intermediate of this pathway, is a natural ligand for the human Vγ9Vδ2 T cells and the most potent natural phosphoantigen known to date. Moreover, 5-hydroxypentane-2,3-dione, a metabolite produced by Escherichia coli 1-deoxy-ᴅ-xylulose 5-phosphate synthase (DXS), the first enzyme of the MEP pathway, structurally resembles (S)-4,5-dihydroxy-2,3-pentanedione, a signal molecule implied in bacterial cell communication. In this review, we shed light on the diversity of potential uses of the MEP pathway in antibacterial therapies, starting with an overview of the antibacterials developed for each of its enzymes. Then, we provide insight into HMBPP, its synthetic analogs, and their prodrugs. Finally, we discuss the potential contribution of the MEP pathway to quorum sensing mechanisms. The MEP pathway, providing simultaneously antibacterial drug targets and potent immunostimulants, coupled with its potential role in bacterial cell-cell communication, opens new therapeutic perspectives.
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4
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Herrscher V, Witjaksono C, Buchotte M, Ferret C, Massicot F, Vasse J, Borel F, Behr J, Seemann M. Irreversible Inhibition of IspG, a Target for the Development of New Antimicrobials, by a 2‐Vinyl Analogue of its MEcPP Substrate. Chemistry 2022; 28:e202200241. [DOI: 10.1002/chem.202200241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Vivien Herrscher
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Clea Witjaksono
- Equipe Chimie Biologique et Applications Thérapeutiques Institut de Chimie de Strasbourg UMR 7177 Université de Strasbourg/CNRS 4, rue Blaise Pascal 67070 Strasbourg France
| | - Marie Buchotte
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Claire Ferret
- Equipe Chimie Biologique et Applications Thérapeutiques Institut de Chimie de Strasbourg UMR 7177 Université de Strasbourg/CNRS 4, rue Blaise Pascal 67070 Strasbourg France
| | - Fabien Massicot
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Jean‐Luc Vasse
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Franck Borel
- Univ. Grenoble Alpes, CEA, CNRS, IBS 38000 Grenoble France
| | - Jean‐Bernard Behr
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Myriam Seemann
- Equipe Chimie Biologique et Applications Thérapeutiques Institut de Chimie de Strasbourg UMR 7177 Université de Strasbourg/CNRS 4, rue Blaise Pascal 67070 Strasbourg France
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5
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Yokoyama K, Li D, Pang H. Resolving the Multidecade-Long Mystery in MoaA Radical SAM Enzyme Reveals New Opportunities to Tackle Human Health Problems. ACS BIO & MED CHEM AU 2022; 2:94-108. [PMID: 35480226 PMCID: PMC9026282 DOI: 10.1021/acsbiomedchemau.1c00046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 01/31/2023]
Abstract
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MoaA is one of the
most conserved radical S-adenosyl-l-methionine
(SAM) enzymes, and is found in most organisms in
all three kingdoms of life. MoaA contributes to the biosynthesis of
molybdenum cofactor (Moco), a redox enzyme cofactor used in various
enzymes such as purine and sulfur catabolism in humans and anaerobic
respiration in bacteria. Unlike many other cofactors, in most organisms,
Moco cannot be taken up as a nutrient and requires de novo biosynthesis.
Consequently, Moco biosynthesis has been linked to several human health
problems, such as human Moco deficiency disease and bacterial infections.
Despite
the medical and biological significance, the biosynthetic mechanism
of Moco’s characteristic pyranopterin structure remained elusive
for more than two decades. This transformation requires the actions
of the MoaA radical SAM enzyme and another protein, MoaC. Recently,
MoaA and MoaC functions were elucidated as a radical SAM GTP 3′,8-cyclase
and cyclic pyranopterin monophosphate (cPMP) synthase, respectively.
This finding resolved the key mystery in the field and revealed new
opportunities in studying the enzymology and chemical biology of MoaA
and MoaC to elucidate novel mechanisms in enzyme catalysis or to address
unsolved questions in Moco-related human health problems. Here, we
summarize the recent progress in the functional and mechanistic studies
of MoaA and MoaC and discuss the field’s future directions.
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Affiliation(s)
- Kenichi Yokoyama
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States.,Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Di Li
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Haoran Pang
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
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Saggu GS. Apicoplast Journey and Its Essentiality as a Compartment for Malaria Parasite Survival. Front Cell Infect Microbiol 2022; 12:881825. [PMID: 35463632 PMCID: PMC9022174 DOI: 10.3389/fcimb.2022.881825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
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Lu Z, Wang B, Qiu Z, Zhang R, Zheng J, Jia Z. YdfD, a Lysis Protein of the Qin Prophage, Is a Specific Inhibitor of the IspG-Catalyzed Step in the MEP Pathway of Escherichia coli. Int J Mol Sci 2022; 23:ijms23031560. [PMID: 35163484 PMCID: PMC8835842 DOI: 10.3390/ijms23031560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 11/22/2022] Open
Abstract
Bacterial cryptic prophage (defective prophage) genes are known to drastically influence host physiology, such as causing cell growth arrest or lysis, upon expression. Many phages encode lytic proteins to destroy the cell envelope. As natural antibiotics, only a few lysis target proteins were identified. ydfD is a lytic gene from the Qin cryptic prophage that encodes a 63-amino-acid protein, the ectopic expression of which in Escherichia coli can cause nearly complete cell lysis rapidly. The bacterial 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway is responsible for synthesizing the isoprenoids uniquely required for sustaining bacterial growth. In this study, we provide evidence that YdfD can interact with IspG, a key enzyme involved in the MEP pathway, both in vivo and in vitro. We show that intact YdfD is required for the interaction with IspG to perform its lysis function and that the mRNA levels of ydfD increase significantly under certain stress conditions. Crucially, the cell lysis induced by YdfD can be abolished by the overexpression of ispG or the complementation of the IspG enzyme catalysis product methylerythritol 2,4-cyclodiphosphate. We propose that YdfD from the Qin cryptic prophage inhibits IspG to block the MEP pathway, leading to a compromised cell membrane and cell wall biosynthesis and eventual cell lysis.
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Affiliation(s)
- Zhifang Lu
- College of Chemistry, Beijing Normal University, Beijing 100875, China; (Z.L.); (B.W.); (Z.Q.); (R.Z.)
| | - Biying Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, China; (Z.L.); (B.W.); (Z.Q.); (R.Z.)
| | - Zhiyu Qiu
- College of Chemistry, Beijing Normal University, Beijing 100875, China; (Z.L.); (B.W.); (Z.Q.); (R.Z.)
| | - Ruiling Zhang
- College of Chemistry, Beijing Normal University, Beijing 100875, China; (Z.L.); (B.W.); (Z.Q.); (R.Z.)
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing 100875, China; (Z.L.); (B.W.); (Z.Q.); (R.Z.)
- Correspondence: (J.Z.); (Z.J.)
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada
- Correspondence: (J.Z.); (Z.J.)
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8
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Henkel S, Frohnecke N, Maus D, McConville MJ, Laue M, Blume M, Seeber F. Toxoplasma gondii apicoplast-resident ferredoxin is an essential electron transfer protein for the MEP isoprenoid-biosynthetic pathway. J Biol Chem 2021; 298:101468. [PMID: 34896149 PMCID: PMC8717598 DOI: 10.1016/j.jbc.2021.101468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 11/30/2022] Open
Abstract
Apicomplexan parasites, such as Toxoplasma gondii, are unusual in that each cell contains a single apicoplast, a plastid-like organelle that compartmentalizes enzymes involved in the essential 2C-methyl-D-erythritol 4-phosphate pathway of isoprenoid biosynthesis. The last two enzymatic steps in this organellar pathway require electrons from a redox carrier. However, the small iron-sulfur cluster-containing protein ferredoxin, a likely candidate for this function, has not been investigated in this context. We show here that inducible knockdown of T. gondii ferredoxin results in progressive inhibition of growth and eventual parasite death. Surprisingly, this phenotype is not accompanied by ultrastructural changes in the apicoplast or overall cell morphology. The knockdown of ferredoxin was instead associated with a dramatic decrease in cellular levels of the last two metabolites in isoprenoid biosynthesis, 1-hydroxy-2-methyl-2-(E)- butenyl-4-pyrophosphate, and isomeric dimethylallyl pyrophosphate/isopentenyl pyrophosphate. Ferredoxin depletion was also observed to impair gliding motility, consistent with isoprenoid metabolites being important for dolichol biosynthesis, protein prenylation, and modification of other proteins involved in motility. Significantly, pharmacological inhibition of isoprenoid synthesis of the host cell exacerbated the impact of ferredoxin depletion on parasite replication, suggesting that the slow onset of parasite death after ferredoxin depletion is because of isoprenoid scavenging from the host cell and leading to partial compensation of the depleted parasite metabolites upon ferredoxin knockdown. Overall, these findings show that ferredoxin has an essential physiological function as an electron donor for the 2C-methyl-D-erythritol 4-phosphate pathway and is a potential drug target for apicomplexan parasites.
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Affiliation(s)
- Stephanie Henkel
- Mycotic and Parasitic Agents and Mycobacteria (FG16), Robert Koch Institute, Berlin, Germany
| | - Nora Frohnecke
- Mycotic and Parasitic Agents and Mycobacteria (FG16), Robert Koch Institute, Berlin, Germany
| | - Deborah Maus
- Metabolism of Microbial Pathogens (NG2), Robert Koch Institute, Berlin, Germany
| | - Malcolm J McConville
- Department of Biochemistry and Pharmacology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Melbourne, Australia
| | - Michael Laue
- Advanced Light and Electron Microscopy (ZBS 4), Robert Koch Institute, Berlin, Germany
| | - Martin Blume
- Metabolism of Microbial Pathogens (NG2), Robert Koch Institute, Berlin, Germany; Department of Biochemistry and Pharmacology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Melbourne, Australia
| | - Frank Seeber
- Mycotic and Parasitic Agents and Mycobacteria (FG16), Robert Koch Institute, Berlin, Germany.
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9
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Arnett CH, Bogacz I, Chatterjee R, Yano J, Oyala PH, Agapie T. Mixed-Valent Diiron μ-Carbyne, μ-Hydride Complexes: Implications for Nitrogenase. J Am Chem Soc 2020; 142:18795-18813. [PMID: 32976708 DOI: 10.1021/jacs.0c05920] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Binding of N2 by the FeMo-cofactor of nitrogenase is believed to occur after transfer of 4 e- and 4 H+ equivalents to the active site. Although pulse EPR studies indicate the presence of two Fe-(μ-H)-Fe moieties, the structural and electronic features of this mixed valent intermediate remain poorly understood. Toward an improved understanding of this bioorganometallic cluster, we report herein that diiron μ-carbyne complex (P6ArC)Fe2(μ-H) can be oxidized and reduced, allowing for the first time spectral characterization of two EPR-active Fe(μ-C)(μ-H)Fe model complexes linked by a 2 e- transfer which bear some resemblance to a pair of En and En+2 states of nitrogenase. Both species populate S = 1/2 states at low temperatures, and the influence of valence (de)localization on the spectroscopic signature of the μ-hydride ligand was evaluated by pulse EPR studies. Compared to analogous data for the {Fe2(μ-H)}2 state of FeMoco (E4(4H)), the data and analysis presented herein suggest that the hydride ligands in E4(4H) bridge isovalent (most probably FeIII) metal centers. Although electron transfer involves metal-localized orbitals, investigations of [(P6ArC)Fe2(μ-H)]+1 and [(P6ArC)Fe2(μ-H)]-1 by pulse EPR revealed that redox chemistry induces significant changes in Fe-C covalency (-50% upon 2 e- reduction), a conclusion further supported by X-ray absorption spectroscopy, 57Fe Mössbauer studies, and DFT calculations. Combined, our studies demonstrate that changes in covalency buffer against the accumulation of excess charge density on the metals by partially redistributing it to the bridging carbon, thereby facilitating multielectron transformations.
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Affiliation(s)
- Charles H Arnett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Theodor Agapie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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10
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McSkimming A, Sridharan A, Thompson NB, Müller P, Suess DLM. An [Fe 4S 4] 3+-Alkyl Cluster Stabilized by an Expanded Scorpionate Ligand. J Am Chem Soc 2020; 142:14314-14323. [PMID: 32692919 DOI: 10.1021/jacs.0c06334] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alkyl-ligated iron-sulfur clusters in the [Fe4S4]3+ charge state have been proposed as short-lived intermediates in a number of enzymatic reactions. To better understand the properties of these intermediates, we have prepared and characterized the first synthetic [Fe4S4]3+-alkyl cluster. Isolation of this highly reactive species was made possible by the development of an expanded scorpionate ligand suited to the encapsulation of cuboidal clusters. Like the proposed enzymatic intermediates, this synthetic [Fe4S4]3+-alkyl cluster adopts an S = 1/2 ground state with giso > 2. Mössbauer spectroscopic studies reveal that the alkylated Fe has an unusually low isomer shift, which reflects the highly covalent Fe-C bond and the localization of Fe3+ at the alkylated site in the solid state. Paramagnetic 1H NMR studies establish that this valence localization persists in solution at physiologically relevant temperatures, an effect that has not been observed for [Fe4S4]3+ clusters outside of a protein. These findings establish the unusual electronic-structure effects imparted by the strong-field alkyl ligand and lay the foundation for understanding the electronic structures of [Fe4S4]3+-alkyl intermediates in biology.
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Affiliation(s)
- Alex McSkimming
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Arun Sridharan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Niklas B Thompson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Peter Müller
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel L M Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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11
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Ye M, Thompson NB, Brown AC, Suess DLM. A Synthetic Model of Enzymatic [Fe 4S 4]-Alkyl Intermediates. J Am Chem Soc 2019; 141:13330-13335. [PMID: 31373801 PMCID: PMC6748666 DOI: 10.1021/jacs.9b06975] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Although
alkyl complexes of [Fe4S4] clusters
have been invoked as intermediates in a number of enzymatic reactions,
obtaining a detailed understanding of their reactivity patterns and
electronic structures has been difficult owing to their transient
nature. To address this challenge, we herein report the synthesis
and characterization of a 3:1 site-differentiated [Fe4S4]2+–alkyl cluster. Whereas [Fe4S4]2+ clusters typically exhibit pairwise delocalized
electronic structures in which each Fe has a formal valence of 2.5+,
Mössbauer spectroscopic and computational studies suggest that
the highly electron-releasing alkyl group partially localizes the
charge distribution within the cubane, an effect that has not been
previously observed in tetrahedrally coordinated [Fe4S4] clusters.
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Affiliation(s)
- Mengshan Ye
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Niklas B Thompson
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Alexandra C Brown
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Daniel L M Suess
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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12
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Colaneri MJ, Vitali J. Probing Axial Water Bound to Copper in Tutton Salt Using Single Crystal 17O-ESEEM Spectroscopy. J Phys Chem A 2018; 122:6214-6224. [PMID: 29989412 DOI: 10.1021/acs.jpca.8b04075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Electron spin-echo envelope modulation (ESEEM) signals attributed to axial water bound to Cu2+ have been detected and analyzed in Cu(II)-doped 17O-water-enriched potassium zinc sulfate hexahydrate (Tutton salt) crystals. The magnetic field orientation dependences of low frequency modulations were measured to fit hyperfine and quadrupole coupling tensors of a 17O ( I = 5/2) nucleus. The hyperfine tensor ( A xx, A yy, A zz: 0.13, 0.23, -3.81 MHz) exhibits almost axial symmetry with the largest value directed normal to the metal equatorial plane in the host structure. Comparisons with quantum chemical calculations position this nucleus about 2.3 Å from the copper. The isotropic coupling (-1.15 MHz) is small and reflects the weak axial water interaction with a dx2-y2 unshared orbital of copper. The 17O-water quadrupole interaction parameters ( e2 qQ/ h = 6.4 MHz and η = 0.93) are close to the average of those found in a variety of solid hydrates. In addition, the coupling tensor directions correlate very closely with the O8 water geometry, with the maximum quadrupole direction 3° from the water plane normal, and its minimum coupling about 2° from the H-H direction. In almost all previous magnetic resonance 17O-water studies, the quadrupole tensor orientation was based on theoretical considerations. This work represents one of the few experimental confirmations of its principal axis frame. When Cu2+ dopes into the Tutton salt, a Jahn-Teller distortion interchanges the relative long and intermediate metal O7 and O8 bond lengths of the zinc host. Therefore, only those unit cells containing the impurity conform to the pure copper Tutton structure. This study provides further support for this model. Moreover, coupling interactions from distant H217O such as in the present case have important implications in studies of copper enzymes and proteins where substrates have been proposed to displace weakly bound water in the active site.
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Affiliation(s)
- Michael J Colaneri
- Department of Chemistry and Physics , State University of New York at Old Westbury , Old Westbury , New York 11568 , United States
| | - Jacqueline Vitali
- Department of Physics and Department of Biological, Geological and Environmental Sciences , Cleveland State University , Cleveland , Ohio 44115 , United States
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13
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Affiliation(s)
- Annika Frank
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Michael Groll
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
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14
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Saggu GS, Pala ZR, Garg S, Saxena V. New Insight into Isoprenoids Biosynthesis Process and Future Prospects for Drug Designing in Plasmodium. Front Microbiol 2016; 7:1421. [PMID: 27679614 PMCID: PMC5020098 DOI: 10.3389/fmicb.2016.01421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/26/2016] [Indexed: 12/20/2022] Open
Abstract
The MEP (Methyl Erythritol Phosphate) isoprenoids biosynthesis pathway is an attractive drug target to combat malaria, due to its uniqueness and indispensability for the parasite. It is functional in the apicoplast of Plasmodium and its products get transported to the cytoplasm, where they participate in glycoprotein synthesis, electron transport chain, tRNA modification and several other biological processes. Several compounds have been tested against the enzymes involved in this pathway and amongst them Fosmidomycin, targeted against IspC (DXP reductoisomerase) enzyme and MMV008138 targeted against IspD enzyme have shown good anti-malarial activity in parasite cultures. Fosmidomycin is now-a-days prescribed clinically, however, less absorption, shorter half-life, and toxicity at higher doses, limits its use as an anti-malarial. The potential of other enzymes of the pathway as candidate drug targets has also been determined. This review details the various drug molecules tested against these targets with special emphasis to Plasmodium. We corroborate that MEP pathway functional within the apicoplast of Plasmodium is a major drug target, especially during erythrocytic stages. However, the major bottlenecks, bioavailability and toxicity of the new molecules needs to be addressed, before considering any new molecule as a potent antimalarial.
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Affiliation(s)
- Gagandeep S Saggu
- Molecular Parasitology and Systems Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science Pilani, India
| | - Zarna R Pala
- Molecular Parasitology and Systems Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science Pilani, India
| | - Shilpi Garg
- Molecular Parasitology and Systems Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science Pilani, India
| | - Vishal Saxena
- Molecular Parasitology and Systems Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science Pilani, India
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15
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Dong M, Horitani M, Dzikovski B, Pandelia ME, Krebs C, Freed JH, Hoffman BM, Lin H. Organometallic Complex Formed by an Unconventional Radical S-Adenosylmethionine Enzyme. J Am Chem Soc 2016; 138:9755-8. [PMID: 27465315 DOI: 10.1021/jacs.6b04155] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Pyrococcus horikoshii Dph2 (PhDph2) is an unusual radical S-adenosylmethionine (SAM) enzyme involved in the first step of diphthamide biosynthesis. It catalyzes the reaction by cleaving SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. To probe the reaction mechanism, we synthesized a SAM analogue (SAMCA), in which the ACP group of SAM is replaced with a 3-carboxyallyl group. SAMCA is cleaved by PhDph2, yielding a paramagnetic (S = 1/2) species, which is assigned to a complex formed between the reaction product, α-sulfinyl-3-butenoic acid, and the [4Fe-4S] cluster. Electron-nuclear double resonance (ENDOR) measurements with (13)C and (2)H isotopically labeled SAMCA support a π-complex between the C═C double bond of α-sulfinyl-3-butenoic acid and the unique iron of the [4Fe-4S] cluster. This is the first example of a radical SAM-related [4Fe-4S](+) cluster forming an organometallic complex with an alkene, shedding additional light on the mechanism of PhDph2 and expanding our current notions for the reactivity of [4Fe-4S] clusters in radical SAM enzymes.
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Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Masaki Horitani
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University , Waltham, Massachusetts 02453, United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States.,Howard Hughes Medical Institute, Cornell University , Ithaca, New York 14853, United States
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16
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Abdel-Azeim S, Jedidi A, Eppinger J, Cavallo L. Mechanistic insights into the reductive dehydroxylation pathway for the biosynthesis of isoprenoids promoted by the IspH enzyme. Chem Sci 2015; 6:5643-5651. [PMID: 28757951 PMCID: PMC5511988 DOI: 10.1039/c5sc01693b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/22/2015] [Indexed: 11/21/2022] Open
Abstract
Here, we report an integrated quantum mechanics/molecular mechanics (QM/MM) study of the bio-organometallic reaction pathway of the 2H+/2e- reduction of (E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate (HMBPP) into the so called universal terpenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), promoted by the IspH enzyme. Our results support the viability of the bio-organometallic pathway through rotation of the OH group of HMBPP away from the [Fe4S4] cluster at the core of the catalytic site, to become engaged in a H-bond with Glu126. This rotation is synchronous with π-coordination of the C2[double bond, length as m-dash]C3 double bond of HMBPP to the apical Fe atom of the [Fe4S4] cluster. Dehydroxylation of HMBPP is triggered by a proton transfer from Glu126 to the OH group of HMBPP. The reaction pathway is completed by competitive proton transfer from the terminal phosphate group to the C2 or C4 atom of HMBPP.
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Affiliation(s)
- Safwat Abdel-Azeim
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Abdesslem Jedidi
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Jorg Eppinger
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Luigi Cavallo
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
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17
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Brown AC, Kokoczka R, Parish T. LytB1 and LytB2 of Mycobacterium tuberculosis Are Not Genetically Redundant. PLoS One 2015; 10:e0135638. [PMID: 26309039 PMCID: PMC4550268 DOI: 10.1371/journal.pone.0135638] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/23/2015] [Indexed: 11/26/2022] Open
Abstract
Mycobacterium tuberculosis synthesises isoprenoid precursors via the MEP/DOXP pathway and at least five enzymes in the pathway (Dxs1, Dxr/IspC, IspD, IspF, and GcpE/IspG) are required for growth in vitro. We investigated the role of LytB (IspH) in M. tuberculosis; M. tuberculosis is unusual in that it has two homologs–LytB1 and LytB2. We were unable to delete the lytB2 gene unless we provided an additional copy elsewhere, demonstrating that this is the essential homolog. We expressed lytB1 from the lytB2 promoter and confirmed that this could not complement for loss of function of lytB2, despite LytB1 possessing all the previously described conserved critical residues. Interestingly the sole LytB homolog of Mycobacterium smegmatis was able to compensate for loss of LytB2 in M. tuberculosis. We tested translational fusions of LytB1 and LytB2 for functionality in M. tuberculosis, but only a fusion with 90% N-terminal LytB2 and 10% C-terminal LytB1 was functional. In order to identify the key difference between the two proteins, site directed mutagenesis was used to change LytB2 residues into their counterparts in LytB1. None of these amino acid substitutions was essential for function and all lytB2 mutant alleles were functional. In contrast, mutation of the key residues for [Fe4S4] cluster formation, as well as a catalytic residue in LytB1 did not result in functional complementation. Thus, although LytB1 and LytB2 are not genetically redundant, this is not dependent on small amino acid changes, but is likely to be a result of major overall structural differences.
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Affiliation(s)
- Amanda Claire Brown
- Queen Mary University of London, London, E1 2AD, United Kingdom
- Barts & the London School of Medicine and Dentistry, London, E1 2AD, United Kingdom
| | - Rachel Kokoczka
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, 98102, United States of America
| | - Tanya Parish
- Queen Mary University of London, London, E1 2AD, United Kingdom
- Barts & the London School of Medicine and Dentistry, London, E1 2AD, United Kingdom
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, 98102, United States of America
- * E-mail:
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18
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Quitterer F, Frank A, Wang K, Rao G, O'Dowd B, Li J, Guerra F, Abdel-Azeim S, Bacher A, Eppinger J, Oldfield E, Groll M. Atomic-Resolution Structures of Discrete Stages on the Reaction Coordinate of the [Fe4S4] Enzyme IspG (GcpE). J Mol Biol 2015; 427:2220-8. [PMID: 25868383 DOI: 10.1016/j.jmb.2015.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/30/2015] [Accepted: 04/02/2015] [Indexed: 11/16/2022]
Abstract
IspG is the penultimate enzyme in non-mevalonate biosynthesis of the universal terpene building blocks isopentenyl diphosphate and dimethylallyl diphosphate. Its mechanism of action has been the subject of numerous studies but remained unresolved due to difficulties in identifying distinct reaction intermediates. Using a moderate reducing agent and an epoxide substrate analogue, we were now able to trap and crystallographically characterize various stages in the IspG-catalyzed conversion of 2-C-methyl-D-erythritol-2,4-cyclo-diphosphate into (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate. In addition, the enzyme's structure was determined in complex with several inhibitors. These results, combined with recent electron paramagnetic resonance data, allowed us to deduce a detailed and complete IspG catalytic mechanism, which describes all stages from initial ring opening to formation of (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate via discrete radical and carbanion intermediates. The data presented in this article provide a guide for the design of selective drugs against many prokaryotic and eukaryotic pathogens to which the non-mevalonate pathway is essential for survival and virulence.
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Affiliation(s)
- Felix Quitterer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany
| | - Annika Frank
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany
| | - Ke Wang
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Guodong Rao
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Bing O'Dowd
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Jikun Li
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Francisco Guerra
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Safwat Abdel-Azeim
- Division of Physical Sciences and Engineering, KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - Adelbert Bacher
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany
| | - Jörg Eppinger
- Division of Physical Sciences and Engineering, KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Michael Groll
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany
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19
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Rekittke I, Warkentin E, Jomaa H, Ermler U. Structure of the GcpE-HMBPP complex from Thermus thermophilius. Biochem Biophys Res Commun 2015; 458:246-50. [DOI: 10.1016/j.bbrc.2015.01.088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 01/19/2015] [Indexed: 11/28/2022]
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20
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Cutsail GE, Telser J, Hoffman BM. Advanced paramagnetic resonance spectroscopies of iron-sulfur proteins: Electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1370-94. [PMID: 25686535 DOI: 10.1016/j.bbamcr.2015.01.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/29/2015] [Accepted: 01/29/2015] [Indexed: 12/20/2022]
Abstract
The advanced electron paramagnetic resonance (EPR) techniques, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) spectroscopies, provide unique insights into the structure, coordination chemistry, and biochemical mechanism of nature's widely distributed iron-sulfur cluster (FeS) proteins. This review describes the ENDOR and ESEEM techniques and then provides a series of case studies on their application to a wide variety of FeS proteins including ferredoxins, nitrogenase, and radical SAM enzymes. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- George E Cutsail
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joshua Telser
- Department of Biological, Chemical and Physical Sciences, Roosevelt University, Chicago, IL 60605, USA
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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21
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Masini T, Hirsch AKH. Development of Inhibitors of the 2C-Methyl-d-erythritol 4-Phosphate (MEP) Pathway Enzymes as Potential Anti-Infective Agents. J Med Chem 2014; 57:9740-63. [DOI: 10.1021/jm5010978] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tiziana Masini
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
7, NL-9747
AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
7, NL-9747
AG Groningen, The Netherlands
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22
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Bhuyan R, Nandy SK, Seal A. Anin silicostructural insights intoPlasmodiumLytB protein and its inhibition. J Biomol Struct Dyn 2014; 33:1198-210. [DOI: 10.1080/07391102.2014.938248] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Yang W, Fu Q, Zhao J, Cheng HR, Shi YC. Two Fe3(μ3-S)2(CO)8 clusters with terminal N-heterocyclic carbenes. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2014; 70:528-32. [PMID: 24898951 DOI: 10.1107/s2053229614009310] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 04/25/2014] [Indexed: 11/10/2022]
Abstract
The title compounds with terminal N-heterocyclic carbenes, namely octacarbonyl(imidazolidinylidene-κC(2))di-μ3-sulfido-triiron(II)(2 Fe-Fe), [Fe3(C3H6N2)(μ3-S)2(CO)8], (I), and octacarbonyl(1-methylimidazo[1,5-a]pyridin-3-ylidene-κC(3))di-μ3-sulfido-triiron(II)(2 Fe-Fe), [Fe3(C8H8N2)(μ3-S)2(CO)8], (II), have been synthesized. Each compound contains two Fe-Fe bonds and two S atoms above and below a triiron triangle. One of the eight carbonyl ligands deviates significantly from linearity. In (I), dimers generated by an N-H···S hydrogen bond are linked into [001] double chains by a second N-H···S hydrogen bond. These chains are packed by a C-H···O hydrogen bond to yield [101] sheets. In (II), dimers generated by an N-H···S hydrogen bond are linked by C-H···O hydrogen bonds to form [111] double chains.
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Affiliation(s)
- Wei Yang
- College of Chemistry and Chemical Engineering, Yangzhou University, 180 Si Wang Ting Road, Yangzhou 225002, People's Republic of China
| | - Qiang Fu
- College of Chemistry and Chemical Engineering, Yangzhou University, 180 Si Wang Ting Road, Yangzhou 225002, People's Republic of China
| | - Jing Zhao
- College of Chemistry and Chemical Engineering, Yangzhou University, 180 Si Wang Ting Road, Yangzhou 225002, People's Republic of China
| | - Huan-Ren Cheng
- College of Chemistry and Chemical Engineering, Yangzhou University, 180 Si Wang Ting Road, Yangzhou 225002, People's Republic of China
| | - Yao-Cheng Shi
- College of Chemistry and Chemical Engineering, Yangzhou University, 180 Si Wang Ting Road, Yangzhou 225002, People's Republic of China
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24
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Span I, Wang K, Eisenreich W, Bacher A, Zhang Y, Oldfield E, Groll M. Insights into the binding of pyridines to the iron-sulfur enzyme IspH. J Am Chem Soc 2014; 136:7926-32. [PMID: 24813236 PMCID: PMC4063180 DOI: 10.1021/ja501127j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Indexed: 11/29/2022]
Abstract
(E)-1-Hydroxy-2-methylbut-2-enyl 4-diphosphate reductase (IspH) is a [Fe4S4] cluster-containing enzyme involved in isoprenoid biosynthesis in many bacteria as well as in malaria parasites and is an important drug target. Several inhibitors including amino and thiol substrate analogues, as well as acetylene and pyridine diphosphates, have been reported. Here, we investigate the mode of binding of four pyridine diphosphates to Escherichia coli IspH by using X-ray crystallography. In three cases, one of the iron atoms in the cluster is absent, but in the structure with (pyridin-3-yl)methyl diphosphate, the most potent pyridine-analogue inhibitor reported previously, the fourth iron of the [Fe4S4] cluster is present and interacts with the pyridine ring of the ligand. Based on the results of quantum chemical calculations together with the crystallographic results we propose a side-on η(2) coordination of the nitrogen and the carbon in the 2-position of the pyridine ring to the unique fourth iron in the cluster, which is in the reduced state. The X-ray structure enables excellent predictions using density functional theory of the (14)N hyperfine coupling and quadrupole coupling constants reported previously using HYSCORE spectroscopy, as well as providing a further example of the ability of such [Fe4S4]-containing proteins to form organometallic complexes.
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Affiliation(s)
- Ingrid Span
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Ke Wang
- Department
of Chemistry, 600 South
Mathews Avenue, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wolfgang Eisenreich
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Adelbert Bacher
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Yong Zhang
- Department
of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology, Castle Point on Hudson, Hoboken, New Jersey 07030, United States
| | - Eric Oldfield
- Department
of Chemistry, 600 South
Mathews Avenue, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Michael Groll
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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25
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Wang W, Oldfield E. Biometallorganische Chemie mit IspG und IspH: Struktur, Funktion und Hemmung der an der Isoprenoid-Biosynthese beteiligten [Fe 4S 4]-Proteine. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201306712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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26
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Wang W, Oldfield E. Bioorganometallic chemistry with IspG and IspH: structure, function, and inhibition of the [Fe(4)S(4)] proteins involved in isoprenoid biosynthesis. Angew Chem Int Ed Engl 2014; 53:4294-310. [PMID: 24481599 DOI: 10.1002/anie.201306712] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Indexed: 11/12/2022]
Abstract
Enzymes of the methylerythritol phosphate pathway of isoprenoid biosynthesis are attractive anti-infective drug targets. The last two enzymes of this pathway, IspG and IspH, are [Fe4 S4 ] proteins that are not produced by humans and catalyze 2 H(+) / 2 e(-) reductions with novel mechanisms. In this Review, we summarize recent advances in structural, mechanistic, and inhibitory studies of these two enzymes. In particular, mechanistic proposals involving bioorganometallic intermediates are presented, and compared with other mechanistic possibilities. In addition, inhibitors based on substrate analogues as well as developed by rational design and compound-library screening, are discussed. The results presented support bioorganometallic catalytic mechanisms for IspG and IspH, and open up new routes to anti-infective drug design targeting [Fe4 S4 ] clusters in proteins.
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Affiliation(s)
- Weixue Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (USA)
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27
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Affiliation(s)
| | - Salim Al-Babili
- BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Eleanore T. Wurtzel
- The Graduate School and University Center, The City University of New York, New York, New York, USA
- Department of Biological Sciences, Lehman College, The City University of New York, Bronx, New York, USA
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28
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Guerra F, Wang K, Li J, Wang W, Liu YL, Amin S, Oldfield E. Inhibition of the 4Fe-4S Proteins IspG and IspH: an EPR, ENDOR and HYSCORE Investigation. Chem Sci 2014; 5:1642-1649. [PMID: 24999381 DOI: 10.1039/c3sc53301h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
IspG and IspH are proteins that are involved in isoprenoid biosynthesis in most bacteria as well as in malaria parasites and are important drug targets. They contain cubane-type 4Fe-4S clusters that are involved in unusual 2H+/2e- reductions. Here, we report the results of electron paramagnetic resonance spectroscopic investigations of the binding of amino- and thiolo-HMBPP (HMBPP=E-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate) IspH substrate-analog inhibitors to both proteins, as well as the binding of HMBPP and an acetylene diphosphate inhibitor, to IspG. The results show that amino-HMBPP binds to reduced IspH by Fe-C π-bonding with the olefinic carbons interacting with the unique 4th Fe in the 4Fe-4S cluster, quite different to the direct Fe-N ligation seen with the oxidized protein. No such π-complex is observed when amino-HMBPP binds to reduced IspG. No EPR signal is observed with IspH in the presence of dithionite and thiolo-HMBPP, suggesting that the 4Fe-4S cluster is not reduced, consistent with the presence of a 420 nm feature in the absorption spectrum (characteristic of an oxidized cluster). However, with IspG, the EPR spectrum in the presence of dithionite and thiolo-HMBPP is very similar to that seen with HMBPP. The binding of HMBPP to IspG was studied using hyperfine sublevel correlation spectroscopy with 17O and 13C labeled samples: the results rule out direct Fe-O bonding and indicate π-bonding. Finally, the binding to IspG of a potent acetylene diphosphate inhibitor was studied by using electron-nuclear double resonance spectroscopy with 13C labeled ligands: the large hyperfine couplings indicate strong Fe-C π-bonding with the acetylenic group. These results illustrate a remarkable diversity in binding behavior for HMBPP-analog inhibitors, opening up new routes to inhibitor design of interest in the context of anti-bacterial and anti-malarial drug discovery, as well as "cubane-type" metallo-biochemistry, in general.
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Affiliation(s)
- Francisco Guerra
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801
| | - Ke Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801
| | - Jikun Li
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801
| | - Weixue Wang
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801
| | - Yi-Liang Liu
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801
| | - Shivani Amin
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801
| | - Eric Oldfield
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801 ; Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801
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29
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Masini T, Kroezen BS, Hirsch AK. Druggability of the enzymes of the non-mevalonate-pathway. Drug Discov Today 2013; 18:1256-62. [DOI: 10.1016/j.drudis.2013.07.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 06/27/2013] [Accepted: 07/04/2013] [Indexed: 12/13/2022]
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30
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Zhao L, Chang WC, Xiao Y, Liu HW, Liu P. Methylerythritol phosphate pathway of isoprenoid biosynthesis. Annu Rev Biochem 2013; 82:497-530. [PMID: 23746261 DOI: 10.1146/annurev-biochem-052010-100934] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isoprenoids are a class of natural products with more than 55,000 members. All isoprenoids are constructed from two precursors, isopentenyl diphosphate and its isomer dimethylallyl diphosphate. Two of the most important discoveries in isoprenoid biosynthetic studies in recent years are the elucidation of a second isoprenoid biosynthetic pathway [the methylerythritol phosphate (MEP) pathway] and a modified mevalonic acid (MVA) pathway. In this review, we summarize mechanistic insights on the MEP pathway enzymes. Because many isoprenoids have important biological activities, the need to produce them in sufficient quantities for downstream research efforts or commercial application is apparent. Recent advances in both MVA and MEP pathway-based synthetic biology are also illustrated by reviewing the landmark work of artemisinic acid and taxadien-5α-ol production through microbial fermentations.
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Affiliation(s)
- Lishan Zhao
- Amyris, Inc., Emeryville, California 94608, USA.
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31
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Terada T, Hirabayashi K, Liu D, Nakamura T, Wakimoto T, Matsumoto T, Tatsumi K. [3:1] Site-Differentiated [4Fe–4S] Clusters Having One Carboxylate and Three Thiolates. Inorg Chem 2013; 52:11997-2004. [DOI: 10.1021/ic4017596] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tamaki Terada
- Department of Chemistry,
Graduate School of Science, ‡Institute of Transformative Bio-Molecules (WPI-ITbM), and §Research Center
for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kiyohisa Hirabayashi
- Department of Chemistry,
Graduate School of Science, ‡Institute of Transformative Bio-Molecules (WPI-ITbM), and §Research Center
for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Dong Liu
- Department of Chemistry,
Graduate School of Science, ‡Institute of Transformative Bio-Molecules (WPI-ITbM), and §Research Center
for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tomohiko Nakamura
- Department of Chemistry,
Graduate School of Science, ‡Institute of Transformative Bio-Molecules (WPI-ITbM), and §Research Center
for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takuya Wakimoto
- Department of Chemistry,
Graduate School of Science, ‡Institute of Transformative Bio-Molecules (WPI-ITbM), and §Research Center
for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tsuyoshi Matsumoto
- Department of Chemistry,
Graduate School of Science, ‡Institute of Transformative Bio-Molecules (WPI-ITbM), and §Research Center
for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kazuyuki Tatsumi
- Department of Chemistry,
Graduate School of Science, ‡Institute of Transformative Bio-Molecules (WPI-ITbM), and §Research Center
for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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Chang WC, Song H, Liu HW, Liu P. Current development in isoprenoid precursor biosynthesis and regulation. Curr Opin Chem Biol 2013; 17:571-9. [PMID: 23891475 PMCID: PMC4068245 DOI: 10.1016/j.cbpa.2013.06.020] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/12/2013] [Accepted: 06/17/2013] [Indexed: 11/20/2022]
Abstract
Isoprenoids are one of the largest classes of natural products and all of them are constructed from two precursors, isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). For decades, the mevalonic acid (MVA) pathway was proposed to be the only IPP and DMAPP biosynthetic pathway. This review summarizes the newly discovered IPP and DMAPP production pathways since late 1990s, their distribution among different kingdoms, and their roles in secondary metabolite production. These new IPP and DMAPP production pathways include the methylerythritol phosphate (MEP) pathway, a modified MVA pathway, and the 5-methylthioadenosine shunt pathway. Relative to the studies on the MVA pathway, information on the MEP pathway regulation is limited and the mechanistic details of several of its novel transformations remain to be addressed. Current status on both MEP pathway regulation and mechanistic issues is also presented.
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Affiliation(s)
- Wei-chen Chang
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Heng Song
- Department of Chemistry, Boston University, Boston, Massachusetts 02215
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, Massachusetts 02215
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Li J, Wang K, Smirnova TI, Khade RL, Zhang Y, Oldfield E. Isoprenoid Biosynthesis: Ferraoxetane or Allyl Anion Mechanism for IspH Catalysis? Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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34
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Li J, Wang K, Smirnova TI, Khade RL, Zhang Y, Oldfield E. Isoprenoid biosynthesis: ferraoxetane or allyl anion mechanism for IspH catalysis? Angew Chem Int Ed Engl 2013; 52:6522-5. [PMID: 23649534 PMCID: PMC3821072 DOI: 10.1002/anie.201302343] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Jikun Li
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Ke Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801 (USA), Fax: (+1)217-244-0997
| | - Tatyana I. Smirnova
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695 (USA)
| | - Rahul L. Khade
- Department of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology, Castle Point on Hudson, Hoboken NJ 07030 (USA)
| | - Yong Zhang
- Department of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology, Castle Point on Hudson, Hoboken NJ 07030 (USA)
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801 (USA), Fax: (+1)217-244-0997
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35
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Kung Y, Runguphan W, Keasling JD. From fields to fuels: recent advances in the microbial production of biofuels. ACS Synth Biol 2012; 1:498-513. [PMID: 23656227 DOI: 10.1021/sb300074k] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Amid grave concerns over global climate change and with increasingly strained access to fossil fuels, the synthetic biology community has stepped up to the challenge of developing microbial platforms for the production of advanced biofuels. The adoption of gasoline, diesel, and jet fuel alternatives derived from microbial sources has the potential to significantly limit net greenhouse gas emissions. In this effort, great strides have been made in recent years toward the engineering of microorganisms to produce transportation fuels derived from alcohol, fatty acid, and isoprenoid biosynthesis. We provide an overview of the biosynthetic pathways devised in the strain development of biofuel-producing microorganisms. We also highlight many of the commonly used and newly devised engineering strategies that have been employed to identify and overcome pathway bottlenecks and problems of toxicity to maximize production titers.
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Affiliation(s)
- Yan Kung
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Weerawat Runguphan
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Departments of Chemical and Biomolecular Engineering and Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
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36
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Structure of the GcpE (IspG)-MEcPP complex from Thermus thermophilus. FEBS Lett 2012; 586:3452-7. [DOI: 10.1016/j.febslet.2012.07.070] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 07/24/2012] [Accepted: 07/27/2012] [Indexed: 11/22/2022]
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Wang W, Wang K, Span I, Jauch J, Bacher A, Groll M, Oldfield E. Are free radicals involved in IspH catalysis? An EPR and crystallographic investigation. J Am Chem Soc 2012; 134:11225-34. [PMID: 22687151 DOI: 10.1021/ja303445z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The [4Fe-4S] protein IspH in the methylerythritol phosphate isoprenoid biosynthesis pathway is an important anti-infective drug target, but its mechanism of action is still the subject of debate. Here, by using electron paramagnetic resonance (EPR) spectroscopy and (2)H, (17)O, and (57)Fe isotopic labeling, we have characterized and assigned two key reaction intermediates in IspH catalysis. The results are consistent with the bioorganometallic mechanism proposed earlier, and the mechanism is proposed to have similarities to that of ferredoxin, thioredoxin reductase, in that one electron is transferred to the [4Fe-4S](2+) cluster, which then performs a formal two-electron reduction of its substrate, generating an oxidized high potential iron-sulfur protein (HiPIP)-like intermediate. The two paramagnetic reaction intermediates observed correspond to the two intermediates proposed in the bioorganometallic mechanism: the early π-complex in which the substrate's 3-CH(2)OH group has rotated away from the reduced iron-sulfur cluster, and the next, η(3)-allyl complex formed after dehydroxylation. No free radical intermediates are observed, and the two paramagnetic intermediates observed do not fit in a Birch reduction-like or ferraoxetane mechanism. Additionally, we show by using EPR spectroscopy and X-ray crystallography that two substrate analogues (4 and 5) follow the same reaction mechanism.
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Affiliation(s)
- Weixue Wang
- Center for Biophysics and Computational Biology, 607 South Mathews Avenue, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Xu W, Lees NS, Hall D, Welideniya D, Hoffman BM, Duin EC. A closer look at the spectroscopic properties of possible reaction intermediates in wild-type and mutant (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase. Biochemistry 2012; 51:4835-49. [PMID: 22646150 DOI: 10.1021/bi3001215] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate reductase (IspH or LytB) catalyzes the terminal step of the MEP/DOXP pathway where it converts (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP) into the two products, isopentenyl diphosphate and dimethylallyl diphosphate. The reaction involves the reductive elimination of the C4 hydroxyl group, using a total of two electrons. Here we show that the active form of IspH contains a [4Fe-4S] cluster and not the [3Fe-4S] form. Our studies show that the cluster is the direct electron source for the reaction and that a reaction intermediate is bound directly to the cluster. This active form has been trapped in a state, dubbed FeS(A), that was detected by electron paramagnetic resonance (EPR) spectroscopy when one-electron-reduced IspH was incubated with HMBPP. In addition, three mutants of IspH have been prepared and studied, His42, His124, and Glu126 (Aquifex aeolicus numbering), with particular attention paid to the effects on the cluster properties and possible reaction intermediates. None of the mutants significantly affected the properties of the [4Fe-4S](+) cluster, but different effects were observed when one-electron-reduced forms were incubated with HMBPP. Replacing His42 led to an increased K(M) value and a much lower catalytic efficiency, confirming the role of this residue in substrate binding. Replacing the His124 also resulted in a lower catalytic efficiency. In this case, however, the enzyme showed the loss of the [4Fe-4S](+) EPR signal upon addition of HMBPP without the subsequent formation of the FeS(A) signal. Instead, a radical-type signal was observed in some of the samples, indicating that this residue plays a role in the correct positioning of the substrate. The incorrect orientation in the mutant leads to the formation of substrate-based radicals instead of the cluster-bound intermediate complex FeS(A). Replacing the Glu126 also resulted in a lower catalytic efficiency, with yet a third type of EPR signal being detected upon incubation with HMBPP. (31)P and (2)H ENDOR measurements of the FeS(A) species incubated with regular and (2)H-C4-labeled HMBPP reveal that the substrate binds to the enzyme in the proximity of the active-site cluster with C4 adjacent to the site of linkage between the FeS cluster and HMBPP. Comparison of the spectroscopic properties of this intermediate to those of intermediates detected in (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase and ferredoxin:thioredoxin reductase suggests that HMBPP binds to the FeS cluster via its hydroxyl group instead of a side-on binding as previously proposed for the species detected in the inactive Glu126 variant. Consequences for the IspH reaction mechanism are discussed.
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Affiliation(s)
- Weiya Xu
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
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39
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Structure, function and inhibition of the two- and three-domain 4Fe-4S IspG proteins. Proc Natl Acad Sci U S A 2012; 109:8558-63. [PMID: 22586085 DOI: 10.1073/pnas.1121107109] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
IspG is a 4Fe4S protein involved in isoprenoid biosynthesis. Most bacterial IspGs contain two domains: a TIM barrel (A) and a 4Fe4S domain (B), but in plants and malaria parasites, there is a large insert domain (A*) whose structure and function are unknown. We show that bacterial IspGs function in solution as (AB)(2) dimers and that mutations in either both A or both B domains block activity. Chimeras harboring an A-mutation in one chain and a B-mutation in the other have 50% of the activity seen in wild-type protein, because there is still one catalytically active AB domain. However, a plant IspG functions as an AA*B monomer. We propose, using computational modeling and electron microscopy, that the A* insert domain has a TIM barrel structure that interacts with the A domain. This structural arrangement enables the A and B domains to interact in a "cup and ball" manner during catalysis, just as in the bacterial systems. EPR/HYSCORE spectra of reaction intermediate, product, and inhibitor ligands bound to both two and three domain proteins are identical, indicating the same local electronic structure, and computational docking indicates these ligands bridge both A and B domains. Overall, the results are of broad general interest because they indicate the insert domain in three-domain IspGs is a second TIM barrel that plays a structural role and that the pattern of inhibition of both two and three domain proteins are the same, results that can be expected to be of use in drug design.
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40
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Citron CA, Brock NL, Rabe P, Dickschat JS. Der stereochemische Verlauf und Mechanismus der IspH-Reaktion. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201110] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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41
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Citron CA, Brock NL, Rabe P, Dickschat JS. The Stereochemical Course and Mechanism of the IspH Reaction. Angew Chem Int Ed Engl 2012; 51:4053-7. [DOI: 10.1002/anie.201201110] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Indexed: 11/06/2022]
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42
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Hale I, O'Neill PM, Berry NG, Odom A, Sharma R. The MEP pathway and the development of inhibitors as potential anti-infective agents. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md00298a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Gräwert T, Groll M, Rohdich F, Bacher A, Eisenreich W. Biochemistry of the non-mevalonate isoprenoid pathway. Cell Mol Life Sci 2011; 68:3797-814. [PMID: 21744068 PMCID: PMC11114746 DOI: 10.1007/s00018-011-0753-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 05/26/2011] [Accepted: 06/14/2011] [Indexed: 02/08/2023]
Abstract
The non-mevalonate pathway of isoprenoid (terpenoid) biosynthesis is essential in many eubacteria including the major human pathogen, Mycobacterium tuberculosis, in apicomplexan protozoa including the Plasmodium spp. causing malaria, and in the plastids of plants. The metabolic route is absent in humans and is therefore qualified as a promising target for new anti-infective drugs and herbicides. Biochemical and structural knowledge about all enzymes involved in the pathway established the basis for discovery and development of inhibitors by high-throughput screening of compound libraries and/or structure-based rational design.
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Affiliation(s)
- Tobias Gräwert
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Michael Groll
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | | | - Adelbert Bacher
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Wolfgang Eisenreich
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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Oldfield E, Lin FY. Terpene biosynthesis: modularity rules. Angew Chem Int Ed Engl 2011; 51:1124-37. [PMID: 22105807 DOI: 10.1002/anie.201103110] [Citation(s) in RCA: 240] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Indexed: 01/10/2023]
Abstract
Terpenes are the largest class of small-molecule natural products on earth, and the most abundant by mass. Here, we summarize recent developments in elucidating the structure and function of the proteins involved in their biosynthesis. There are six main building blocks or modules (α, β, γ, δ, ε, and ζ) that make up the structures of these enzymes: the αα and αδ head-to-tail trans-prenyl transferases that produce trans-isoprenoid diphosphates from C(5) precursors; the ε head-to-head prenyl transferases that convert these diphosphates into the tri- and tetraterpene precursors of sterols, hopanoids, and carotenoids; the βγ di- and triterpene synthases; the ζ head-to-tail cis-prenyl transferases that produce the cis-isoprenoid diphosphates involved in bacterial cell wall biosynthesis; and finally the α, αβ, and αβγ terpene synthases that produce plant terpenes, with many of these modular enzymes having originated from ancestral α and β domain proteins. We also review progress in determining the structure and function of the two 4Fe-4S reductases involved in formation of the C(5) diphosphates in many bacteria, where again, highly modular structures are found.
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Affiliation(s)
- Eric Oldfield
- Department of Chemistry and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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46
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Smith JM, Vierling RJ, Meyers CF. Selective inhibition of E. coli 1-deoxy-D-xylulose-5-phosphate synthase by acetylphosphonates(). MEDCHEMCOMM 2011; 3:65-67. [PMID: 23326631 DOI: 10.1039/c1md00233c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DXP synthase catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate, an essential precursor in pathogen isoprenoid biosynthesis. The selective inhibition of this ThDP-dependent transformation is a challenging goal in the development of isoprenoid biosynthesis inhibitors. Potent, selective inhibitors could lead to new anti-infective agents. Here, we demonstrate selective inhibition of E. coli DXP synthase by butylacetylphosphonate.
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Affiliation(s)
- Jessica M Smith
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
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47
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Xiao Y, Chang WC, Liu HW, Liu P. Study of IspH, a key enzyme in the methylerythritol phosphate pathway using fluoro-substituted substrate analogues. Org Lett 2011; 13:5912-5. [PMID: 21981393 DOI: 10.1021/ol202559r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
IspH, a [4Fe-4S]-cluster-containing enzyme, catalyzes the reductive dehydroxylation of 4-hydroxy-3-methyl-butenyl diphosphate (HMBPP) to isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the methylerythritol phosphate pathway. Studies of IspH using fluoro-substituted substrate analogues to dissect the contributions of several factors to IspH catalysis, including the coordination of the HMBPP C(4)-OH group to the iron-sulfur cluster, the H-bonding network in the active site, and the electronic properties of the substrates, are reported.
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Affiliation(s)
- Youli Xiao
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
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48
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Wang W, Wang K, Li J, Nellutla S, Smirnova TI, Oldfield E. An ENDOR and HYSCORE investigation of a reaction intermediate in IspG (GcpE) catalysis. J Am Chem Soc 2011; 133:8400-3. [PMID: 21574560 DOI: 10.1021/ja200763a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
IspG is a 4Fe-4S protein that carries out an essential reduction step in isoprenoid biosynthesis. Using electron-nuclear double resonance (ENDOR) and hyperfine sublevel correlation (HYSCORE) spectroscopies on labeled samples, we have specifically assigned the hyperfine interactions in a reaction intermediate. These results help clarify the nature of the reaction intermediate, supporting a direct interaction between the unique fourth Fe in the cluster and C2 and O3 of the ligand.
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Affiliation(s)
- Weixue Wang
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, Illinois 61801, USA
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49
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Dairi T, Kuzuyama T, Nishiyama M, Fujii I. Convergent strategies in biosynthesis. Nat Prod Rep 2011; 28:1054-86. [PMID: 21547300 DOI: 10.1039/c0np00047g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This review article focuses on how nature sometimes solves the same problem in the biosynthesis of small molecules but using very different approaches. Four examples, involving isopentenyl diphosphate, menaquinone, lysine, and aromatic polyketides, are highlighted that represent different strategies in convergent metabolism.
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Affiliation(s)
- Tohru Dairi
- Faculty of Engineering and Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan.
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50
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Baumeister S, Wiesner J, Reichenberg A, Hintz M, Bietz S, Harb OS, Roos DS, Kordes M, Friesen J, Matuschewski K, Lingelbach K, Jomaa H, Seeber F. Fosmidomycin uptake into Plasmodium and Babesia-infected erythrocytes is facilitated by parasite-induced new permeability pathways. PLoS One 2011; 6:e19334. [PMID: 21573242 PMCID: PMC3087763 DOI: 10.1371/journal.pone.0019334] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 03/27/2011] [Indexed: 11/18/2022] Open
Abstract
Background Highly charged compounds typically suffer from low membrane permeability and thus are generally regarded as sub-optimal drug candidates. Nonetheless, the highly charged drug fosmidomycin and its more active methyl-derivative FR900098 have proven parasiticidal activity against erythrocytic stages of the malaria parasite Plasmodium falciparum. Both compounds target the isoprenoid biosynthesis pathway present in bacteria and plastid-bearing organisms, like apicomplexan parasites. Surprisingly, the compounds are inactive against a range of apicomplexans replicating in nucleated cells, including Toxoplasma gondii. Methodology/Principal Findings Since non-infected erythrocytes are impermeable for FR90098, we hypothesized that these drugs are taken up only by erythrocytes infected with Plasmodium. We provide evidence that radiolabeled FR900098 accumulates in theses cells as a consequence of parasite-induced new properties of the host cell, which coincide with an increased permeability of the erythrocyte membrane. Babesia divergens, a related parasite that also infects human erythrocytes and is also known to induce an increase in membrane permeability, displays a similar susceptibility and uptake behavior with regard to the drug. In contrast, Toxoplasma gondii-infected cells do apparently not take up the compounds, and the drugs are inactive against the liver stages of Plasmodium berghei, a mouse malaria parasite. Conclusions/Significance Our findings provide an explanation for the observed differences in activity of fosmidomycin and FR900098 against different Apicomplexa. These results have important implications for future screens aimed at finding new and safe molecular entities active against P. falciparum and related parasites. Our data provide further evidence that parasite-induced new permeability pathways may be exploited as routes for drug delivery.
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Affiliation(s)
- Stefan Baumeister
- Parasitologie, Fachbereich Biologie, Philipps-Universität, Marburg, Germany
| | - Jochen Wiesner
- Institut für Klinische Immunologie und Transfusionsmedizin, Universitätsklinikum Giessen und Marburg GmbH, Giessen, Germany
| | - Armin Reichenberg
- Institut für Klinische Immunologie und Transfusionsmedizin, Universitätsklinikum Giessen und Marburg GmbH, Giessen, Germany
| | - Martin Hintz
- Institut für Klinische Immunologie und Transfusionsmedizin, Universitätsklinikum Giessen und Marburg GmbH, Giessen, Germany
| | - Sven Bietz
- Parasitologie, Fachbereich Biologie, Philipps-Universität, Marburg, Germany
| | - Omar S. Harb
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - David S. Roos
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Maximilian Kordes
- Parasitology Unit, Max-Planck-Institute for Infection Biology, Berlin, Germany
| | - Johannes Friesen
- Parasitology Unit, Max-Planck-Institute for Infection Biology, Berlin, Germany
| | - Kai Matuschewski
- Parasitology Unit, Max-Planck-Institute for Infection Biology, Berlin, Germany
| | - Klaus Lingelbach
- Parasitologie, Fachbereich Biologie, Philipps-Universität, Marburg, Germany
| | - Hassan Jomaa
- Institut für Klinische Immunologie und Transfusionsmedizin, Universitätsklinikum Giessen und Marburg GmbH, Giessen, Germany
| | - Frank Seeber
- Parasitologie, Fachbereich Biologie, Philipps-Universität, Marburg, Germany
- Fachgebiet 16 Parasitologie, Robert-Koch-Institut, Berlin, Germany
- * E-mail:
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